NAME

  GD_Filter_Enzymes.pl

VERSION

  Version 5.51

DESCRIPTION

  Creates a list of restriction enzymes that meet optionally provided criteria.
  Any criteria left blank will not be used to filter the results.

USAGE

  List all enzymes that leave non-1bp overhangs and cut inside recognition seq:
        GD_Filter_Enzymes.pl --sticky 35 --cleavage in

  List all enzymes that are available from NEB or Stratagene and are inactivated
  at or below 60 deg and cost less than 50 cents a unit:
        GD_Filter_Enzymes.pl --vendor N,E --inactivation 60 --pricemax .5

  List all enzymes that have at least 25% activity in NEB buffers 1 and 4 and
  are indifferent to CpG methylation
        GD_Filter_Enzymes.pl --buffer NEB1=25,NEB4=25 --cpgsense indifferent

  List all enzymes that exhibit star activity and are blocked or inhibited by
  Dam methylation
        GD_Filter_Enzymes.pl --staractivity 1 --damsense blocked,inhibited

  List all enzymes that may leave nonpalindromic overhangs (and those that
  definitely do) and whose recognition sequences do not contain AT or TA
        GD_Filter_Enzymes.pl --palindromy pnon,nonpal --seqmaynothave AT,TA

ARGUMENTS

Optional arguments:

  -h,   --help : Display this message
  -enzymelist     : The name of an enzyme set to use in configuration, defaults
                    to standard_and_IIB
  --sticky        : [1, 3, 5, b] What type of overhang is left by the enzyme
  --palindromy    : [pal, pnon, nonpal] Is the overhang left by the enzyme
                    palindromic, potentially non-palindromic, or non-palindromic
  --length        : How many bases long is the recognition site allowed to be,
                    accepts a comma separated list
  --ambiguous     : [nonNonly OR ATCGonly] Are ambiguous bases allowed in the
                    recognition site. If yes to all, don't include this option
  --inactivation  : Enzymes must be inactivated by at least this temperature
  --incubation    : Enzymes must incubate at this temperature
  --staractivity  : [1 OR 0] Enzymes with or without star activity
  --cpgsense      : [blocked, inhibited, indifferent] Sensitivity to CpG
                    methylation
  --damsense      : [blocked, inhibited, indifferent] Sensitivity to Dam
                    methylation
  --dcmsense      : [blocked, inhibited, indifferent] Sensitivity to Dcm
                    methylation
  --buffer        : List of buffer activity thresholds. NEB1=50,NEB2=50 means
                    enzymes must have at least 50% activity in NEB buffers 1 & 2
                    Other=50 will work for non NEB buffers
  --pricemax      : The highest amount in dollars/unit an enzyme can cost
  --seqmusthave   : List of sequences that must be found in the recognition site
  --seqmaynothave : List of sequences that must not be in the recognition site
  --vendor        : List of vendors that must stock the enzyme, using the
                    comma separated abbreviations:
                        B = Invitrogen
                        C = Minotech
                        E = Stratagene
                        F = Thermo Scientific Fermentas
                        I = SibEnzyme
                        J = Nippon Gene Co.
                        K = Takara
                        M = Roche Applied Science
                        N = New England Biolabs
                        O = Toyobo Technologies
                        Q = Molecular Biology Resources
                        R = Promega
                        S = Sigma Aldrich
                        U = Bangalore Genei
                        V = Vivantis
                        X = EURx
                        Y = CinnaGen